// WriteNameToBuffer()
void DataIO_Std::WriteNameToBuffer(CpptrajFile& fileIn, std::string const& label,
int width, bool isLeftCol)
{
std::string temp_name = label;
// If left aligning, add '#' to name;
if (isLeftCol) {
if (temp_name[0]!='#') {
temp_name.insert(0,"#");
// Ensure that name will not be larger than column width.
if ((int)temp_name.size() > width)
temp_name.resize( width );
}
}
// Replace any spaces with underscores
for (std::string::iterator tc = temp_name.begin(); tc != temp_name.end(); ++tc)
if ( *tc == ' ' )
*tc = '_';
if (width >= (int)CpptrajFile::BUF_SIZE)
// Protect against CpptrajFile buffer overflow
fileIn.Write(temp_name.c_str(), temp_name.size());
else {
// Set up header format string
TextFormat::AlignType align;
if (isLeftCol)
align = TextFormat::LEFT;
else
align = TextFormat::RIGHT;
TextFormat header_format(TextFormat::STRING, width, align);
fileIn.Printf(header_format.fmt(), temp_name.c_str());
}
}
// DataIO_CCP4::WriteSet3D()
int DataIO_CCP4::WriteSet3D( DataSetList::const_iterator const& setIn, CpptrajFile& outfile ) {
if ((*setIn)->Size() < 1) return 1; // SANITY CHECK: No empty grid allowed
if ((*setIn)->Ndim() != 3) {
mprinterr("Internal Error: DataSet %s in DataFile %s has %zu dimensions, expected 3.\n",
(*setIn)->legend(), outfile.Filename().full(), (*setIn)->Ndim());
return 1;
}
DataSet_3D const& grid = static_cast<DataSet_3D const&>( *(*setIn) );
// Check input grid
Vec3 OXYZ = grid.GridOrigin();
if (OXYZ[0] < 0.0 || OXYZ[1] < 0.0 || OXYZ[2] < 0.0 ||
OXYZ[0] > 0.0 || OXYZ[1] > 0.0 || OXYZ[2] > 0.0)
mprintf("Warning: Grid '%s' origin is not 0.0, 0.0, 0.0\n"
"Warning: Origin other than 0.0 not yet supported for CCP4 write.\n");
// Set default title if none set
if (title_.empty())
title_.assign("CPPTRAJ CCP4 map volumetric data, set '" + grid.Meta().Legend() +
"'. Format revision A.");
// Check that title is not too big
if (title_.size() > 800) {
mprintf("Warning: CCP4 title is too large, truncating.\n");
title_.resize( 800 );
}
// Set up and write header
headerbyte buffer;
buffer.i[0] = (int)grid.NX();
buffer.i[1] = (int)grid.NY();
buffer.i[2] = (int)grid.NZ();
buffer.i[3] = 2; // Only mode 2 supported
buffer.i[4] = 0; // No offsets
buffer.i[5] = 0;
buffer.i[6] = 0;
buffer.i[7] = (int)grid.NX();
buffer.i[8] = (int)grid.NY();
buffer.i[9] = (int)grid.NZ();
Box box( grid.Ucell() );
buffer.f[10] = (float)box[0];
buffer.f[11] = (float)box[1];
buffer.f[12] = (float)box[2];
buffer.f[13] = (float)box[3];
buffer.f[14] = (float)box[4];
buffer.f[15] = (float)box[5];
buffer.i[16] = 1; // Cols = X
buffer.i[17] = 2; // Rows = Y
buffer.i[18] = 3; // Secs = Z
// Determine min, max, and mean of data
double mean = grid[0];
double gmin = grid[0];
double gmax = grid[0];
double rmsd = grid[0] * grid[0];
for (unsigned int i = 1; i < grid.Size(); i++) {
gmin = std::min(grid[i], gmin);
gmax = std::max(grid[i], gmax);
mean += grid[i];
rmsd += grid[i] * grid[i];
}
mean /= (double)grid.Size();
rmsd /= (double)grid.Size();
rmsd = rmsd - (mean * mean);
if (rmsd > 0.0)
rmsd = sqrt(rmsd);
else
rmsd = 0.0;
mprintf("\t%s\n", title_.c_str());
mprintf("\tDensity: Min=%f Max=%f Mean=%f RMS=%f\n", gmin, gmax, mean, rmsd);
buffer.f[19] = (float)gmin;
buffer.f[20] = (float)gmax;
buffer.f[21] = (float)mean;
buffer.i[22] = 1; // Assume P1
buffer.i[23] = 0; // No bytes for symmetry ops
buffer.i[24] = 0; // No skew transform
// Skew matrix (S11, S12, S13, S21, ...) and translation; 12 total, followed
// by 15 'future use'; zero all.
std::fill( buffer.i+25, buffer.i+52, 0 );
// MAP and machine precision. FIXME determine endianness!
buffer.c[208] = 'M';
buffer.c[209] = 'A';
buffer.c[210] = 'P';
buffer.c[211] = ' ';
buffer.c[212] = 0x44; // little endian
buffer.c[213] = 0x41;
buffer.c[214] = 0x00;
buffer.c[215] = 0x00;
// Determine RMS deviation from mean.
buffer.f[54] = (float)rmsd;
// Determine number of labels being used
buffer.i[55] = (int)title_.size() / 80;
if ( ((int)title_.size() % 80) != 0)
buffer.i[55]++;
outfile.Write( buffer.c, 224*sizeof(unsigned char) );
// Write labels; 10 lines, 80 chars each
outfile.Write( title_.c_str(), title_.size() );
// FIXME this seems wasteful.
std::vector<char> remainder( 800 - title_.size(), 0 );
outfile.Write( &remainder[0], remainder.size() );
remainder.clear();
// No symmetry bytes
// Store data in buffer, then write. X changes fastest.
// SANITY CHECK; This will result in invalid files if size of float is not 4.
if (sizeof(float) != wSize)
mprintf("Warning: Size of float on this system is %zu, not 4.\n"
"Warning: Resulting CCP4 file data will not conform to standard.\n", sizeof(float));
std::vector<float> mapbuffer( grid.Size() );
std::vector<float>::iterator it = mapbuffer.begin();
for (unsigned int iz = 0; iz != grid.NZ(); iz++)
for (unsigned int iy = 0; iy != grid.NY(); iy++)
for (unsigned int ix = 0; ix != grid.NX(); ix++)
*(it++) = grid.GetElement( ix, iy, iz );
outfile.Write( &mapbuffer[0], mapbuffer.size() * sizeof(float) );
outfile.CloseFile();
return 0;
}